MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20)

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	affected	Class	Microarray Measured (#genes)	Accession

Results: HTML CSV LaTeX

Showing element 51 to 100 of 8866 in total

Average Regulation (ratio)	% Affected Genes	Would Be Affected (#genes)	Class Size (#genes)	Class	Class
4.7064167857170105	1.9231	3	135	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	molecular function
	1.6807		151	oxidoreductase activity, acting on CH-OH group of donors
4.679882526397705	25.0000	1	4	outward rectifier potassium channel activity
	8.3333		13	delayed rectifier potassium channel activity
4.620415210723877	2.7027		40	protein amino acid N-linked glycosylation	biological process
4.601345539093018	1.0811	2	225	reproductive process
4.553711891174316	50.0000	1	2	parathyroid hormone receptor activity	molecular function
	3.5714		37	secretin-like receptor activity
4.506189823150635	5.8824		18	phagocytosis	biological process
4.492823123931885	6.6667		20	negative regulation of gene expression, epigenetic
	5.8824		19	nuclear membrane	cellular component
	2.2222		53	regulation of gene expression, epigenetic	biological process
4.407965660095215	14.2857		8	aldehyde dehydrogenase (NAD) activity	molecular function
	1.3333		100	neuropeptide signaling pathway	biological process
4.405977725982666	50.0000		2	GMP reductase activity	molecular function
				oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor
	1.5873		87	oxidoreductase activity, acting on NADH or NADPH
4.290065228939056	3.7037	2	66	histamine receptor activity
4.135706186294556	3.9474	4	90	nucleoplasm	cellular component
4.105485280354817	5.4545		80	humoral immune response	biological process
4.079947471618652	3.4483	1	32	insulin receptor signaling pathway
	3.3333			transport vesicle	cellular component
4.046511650085449	50.0000	2	3	nuclear migration	biological process
	33.3333	1		nuclear chromosome, telomeric region	cellular component
				nuclear membrane organization and biogenesis	biological process
	25.0000	2	6	establishment of nucleus localization
	12.5000	1	9	mitotic spindle organization and biogenesis
	7.6923		16	condensed nuclear chromosome	cellular component
	5.0000		23	chromosome, telomeric region
	2.3256		56	nuclear envelope
4.037245273590088	14.2857		7	transmembrane receptor protein tyrosine phosphatase signaling pathway	biological process
	5.5556		18	transmembrane receptor protein phosphatase activity	molecular function
				transmembrane receptor protein tyrosine phosphatase activity
3.9968204498291016	1.7857		72	vascular endothelial growth factor receptor activity
	1.0309		119	GPI anchor binding
3.9418493509292603	1.5385	3	172	cysteine-type peptidase activity
3.9217323064804077	40.0000	2	5	embryonic skeletal morphogenesis	biological process
	18.1818		13	skeletal morphogenesis
3.895843982696533	1.0309	1	109	Wnt receptor signaling pathway
3.8507699966430664	100.0000	2	2	arylamine N-acetyltransferase activity	molecular function
	4.5455		52	N-acetyltransferase activity
	4.0000		61	N-acyltransferase activity
	3.7736		63	acetyltransferase activity
3.8397669792175293	5.0000	1	21	nuclear matrix	cellular component
3.819567561149597	3.2258	4	133	regulation of cell growth	biological process
3.8173599243164062	2.9412	1	39	transcription initiation from RNA polymerase II promoter
	1.7857		68	transcription initiation
3.789476911226908	4.4118	4	80	structural constituent of cell wall	molecular function
3.749711751937866	12.5000	1	10	glutathione peroxidase activity
	5.2632	2	31	selenium binding

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.